profiles.xml

<?xml version="1.0" standalone="yes"?>


<!--

metav depends on the following software and databases, and you need to prepare them in advance on your computer.
In general, these parameters only need to be configured once in the first running, except for the host database used to filter contamination.

Below is an example, please note:
(1) currently version of metav only supports the sequenced data from second-generation sequencing.
(2) the paths of these databases in this *.xml need to be adjusted with reference to your computer.
(3) generally, the parameters of software in this *.xml file does not need to be modified because they are suitable in most cases.

-->
 

<dependencies>

	<!-- the path of host database which was created in advance by bowtie2-build program, and usually needs to be adjusted. -->
	<!-- for example: bowtie2-build /path/Human_Gallus_gallus.fas /path/Human_Gallus_gallus -->
	<database name="hostdb">
		<path>
		/home/zzj/HTS/host_db/xxx_db/xxx
		</path>
	</database>


	<!-- the path of viral nr database (*.dmnd), which was created in advance by diamond program. -->
	<database name="viral_nr">
		<path>
		/home/zzj/HTS/diamond_data/ViralProtein.dmnd
		</path>
	</database>

	<!-- the path of information of viral taxonomy.  -->
	<taxonomy name="viral_taxonomy">
		<path>
		/home/zzj/HTS/diamond_data/taxonomy_information_2024-06-02.txt
		</path>
	</taxonomy>


	<!-- the parameters of trimmomatic, please adjust the path of merge_adapter.fas -->
	<app name="trimmomatic">
		<parameter>
		ILLUMINACLIP:/home/zzj/anaconda3/envs/metav_env/share/trimmomatic-0.39-2/adapters/merge_adapter.fas:2:40:15:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
		</parameter>
	</app>


	<!-- the parameters of bowtie2 -->
	<app name="bowtie2">
		<parameter>
		--very-sensitive --dovetail
		</parameter>
	</app>


	<!--  the key parameters of Trinity -->
	<app name="Trinity">
		<parameter>
		--max_memory 50G
		</parameter>
	</app>


	<!--  the key parameter of diamond program, note, the e-value is fixed at 1.  -->
	<app name="diamond">
		<paremeter>
		--max-target-seqs 1 -b5 -c1
		</paremeter>
	</app>


</dependencies>

<!--  note, these software and databases dependencies needs to be prepared manually in advance, and these softwares need to be added to PATH (system or user).  -->